soap2bam

soap2bam: A efficient software tools to convert soap to bam/sam format



The newest version of this funtion was integrated into toolkit BamDeal ,please replace soap2bam by this BamDeal.

           ./BamDeal    convert    soap2bam

1. Install

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Please replace soap2bam with this toolkit BamDeal.

 This software rely htslib，so should Pre-install htslib first samtools-1.5/htslib-1.5
Then Just [make] or [sh make.sh ] to compile this software.
the final software can be found in the Dir [bin/soap2bam]

For linux /Unix

        tar -zxvf  soap2bam-XXX.tar.gz
        cd soap2bam-XXX;                             # if Link do not work ,Try re-install two library
        cd src;                                      #【zlib and htslib】 and copy them to the library Dir
        make ; make clean                            # soap2bam-XX/src/include/zlib 
        ../bin/soap2bam                              

For macOS

#step1 :Should must re-install  third  library 【zlib and gzstream htslib】
              see  [zlib and gzstream] website 
#step2  :  # Copy these two library into Dirs 
              cp libz.a libz.so*  soap2bam-XX/src/include/zlib
              cp libgzstream.a  soap2bam-XX/src/include/gzstream
#step3  : 
              sh make.sh # or [make && make clean]

2. Example

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• 1. soap2sam

#To convert soap file to the sam file

     ./bin/soap2bam   -InSoap in.soap  -OutSam out.sam.gz
     ./bin/soap2bam   -InSoap in.soap  -OutSam  out.sam.gz -Dict  Ref.dict
     ./bin/soap2bam   -InSoap in.soap.gz -OutSam  out.sam.gz  -Dict Ref.fa

   1. Soap2bam -i <in.soap> -s AAA
      This will convert the SOAP to SAM and output to a compressed file named AAA in current directory

   2. Soap2bam -i <in.soap> -b AAA -d Ref.fa
      This will convert the SOAP to BAM with the header from reference FASTA and output to a compressed file named AAA in current directory.

• 2. soap2bam

# To convert soap file to the bam file

     ./bin/soap2bam    -InSoap in.soap  -Outbam out.bam  -Dict  Ref.fa
  # Also you the  add the  -ShiftQ  modify the seqQ  for ASCII64 --> ASCII33
     ./bin/soap2bam    -InSoap in.soap  -Outbam out.bam  -Dict  Ref.fa -ShiftQ -31

3. Introduction

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• Parameter description

./BamDeal    convert  soap2bam

        Usage: soap2bam  -i <in.soap> -s <out.sam>
        Usage: soap2bam  -i <in.soap> -b <out.bam> -d Ref.dict

                -i   <str>   input  Soap file
                -b   <str>   output BAM file
                -s   <str>   output SAM file

                -d   <str>   input ref FASTA to get header for BAM
                -p           if soap is PairOut,for flag
                -Q   <int>   shift sequence quality score by [+31] or [-31] or [0], default [0]
                -g           all read in memory to search mate information

                -h           show more help [hewm2008 v1.04]

4. Results

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Format Introduction

• soap format  
  chinese soap introduction
• sam bam format

5）Discussing

• email: [email protected] / [email protected]
• join the QQ Group : 125293663

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